Contacts of the strand formed by residues 70 - 75 (chain L) in PDB entry 2A3W
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 70 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65L LYS* 3.7 8.8 - - - +
66L GLU* 3.6 21.4 + - + +
67L ARG* 2.8 68.8 + - + +
68L VAL 4.4 1.1 - - - +
69L GLY* 1.3 77.0 - - - +
71L TYR* 1.3 64.2 + - - +
81L THR* 3.8 22.4 - - + +
82L SER 3.7 1.1 - - - -
83L LYS* 3.8 38.3 + - + +
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Residues in contact with TYR 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L LEU* 4.4 8.3 - - + -
63L VAL* 5.3 2.2 - - + -
64L TYR 3.8 2.5 - - - -
65L LYS* 3.6 33.3 + - + -
70L GLU* 1.3 80.3 - - - +
72L SER* 1.3 61.6 + - - +
81L THR* 3.3 2.2 - - - -
82L SER 2.9 37.2 + - - +
84L VAL* 3.7 22.9 - - + -
86L GLU* 2.6 31.4 + - - -
92L VAL* 3.8 18.2 - - + +
94L ILE* 3.7 26.5 - - + -
107L PHE* 3.7 33.0 - + + -
109L ILE* 3.7 23.8 - - + -
114L LEU* 4.6 1.8 - - + -
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Residues in contact with SER 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62L LEU 3.5 0.4 - - - +
63L VAL* 3.4 5.0 - - - -
64L TYR* 2.8 46.1 + - - -
66L GLU* 4.6 8.7 - - - +
70L GLU 4.3 0.2 - - - -
71L TYR* 1.3 73.9 - - - +
73L LEU* 1.3 59.6 + - - +
74L TYR* 4.1 21.8 - - - -
79L LYS* 3.6 9.6 - - - -
80L VAL 3.2 7.0 - - - -
81L THR* 2.6 28.8 + - - +
107L PHE* 3.7 7.3 - - - -
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Residues in contact with LEU 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L PHE* 4.3 4.5 - - + -
61L LEU* 3.7 26.0 - - + -
62L LEU 3.3 12.1 - - - +
63L VAL* 4.0 13.2 - - + -
72L SER* 1.3 73.2 - - - +
74L TYR* 1.3 66.3 + - - +
75L ILE* 3.8 22.2 - - + -
78L HIS 3.9 0.5 - - - +
79L LYS* 3.4 1.0 - - - -
80L VAL* 2.8 43.9 + - + +
96L VAL* 4.1 16.4 - - + -
98L TRP* 4.2 8.5 - - + -
105L ALA* 3.7 27.4 - - + -
107L PHE* 3.8 16.0 - - + -
119L LEU* 4.0 4.6 - - + +
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Residues in contact with TYR 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L ASN* 3.8 25.8 - - + +
61L LEU* 3.3 6.8 - - - -
62L LEU* 2.8 63.1 + - + +
64L TYR* 4.0 21.2 - + + -
66L GLU* 5.8 0.3 - - - +
72L SER* 4.1 5.8 - - - -
73L LEU* 1.3 78.7 - - - +
75L ILE* 1.3 66.0 + - - +
77L ARG 3.6 22.4 - - - -
78L HIS 3.0 4.9 - - - +
79L LYS* 3.3 47.5 + - + -
347L CPJ 3.3 40.2 - - + -
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Residues in contact with ILE 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L PHE* 3.6 35.2 - - + -
60L GLU 3.3 6.5 - - - +
61L LEU* 4.3 4.9 - - + -
73L LEU* 3.8 17.7 - - + -
74L TYR* 1.3 80.5 - - - +
76L GLY* 1.3 68.8 + - - +
77L ARG 3.2 0.2 - - - -
78L HIS* 2.8 20.1 + - - +
98L TRP* 3.9 35.9 - - + -
119L LEU* 3.8 17.0 - - + +
120L ARG* 3.1 15.7 - - + -
123L TYR* 3.9 24.2 - - + -
125L VAL* 4.7 5.4 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il